Loss of offset after pertrochanteric hip fractures affects hip function one year after surgery with a short intramedullary nail. A prospective cohort study.

PURPOSE: We hypothesised that protruding collum screws in intramedullary nails used for pertrochanteric fractures cause lateral pain/discomfort and that loss of offset relates to poorer hip function. METHODS: Seventy-six patients with an acute pertrochanteric femoral fracture AO types A1 and A2 were operated upon using a short intramedullary nail and were included in a prospective observational cohort study and followed-up for one year. The main outcome variables were lateral pain and hip function as evaluated with the Harris Hip Score. The main exposure was compression along the collum screw and lateral protrusion measured by anteroposterior X-ray images. Perioperative images were compared to images at the follow-up visit. Outcome variables were adjusted in regression models for reduction, fracture type, body mass index, sex and age. RESULTS: A total of 28 (36 %) patients experienced lateral pain at one year. We found a correlation between lateral protrusion and lateral pain, adjusted OR 4.5 per protruding centimetre (95 % CI, 1.1-17.5). Collum compression correlated with a poorer outcome with Harris Hip Score -14.2 per compressed centimetre (95 % CI, -21.8 to -6.7). CONCLUSIONS: In patients with type A1 and A2 pertrochanteric fractures operated on using intramedullary nailing, a large compression and lateral protrusion of the collum screw are associated with poorer hip function and lateral pain. New technical improvements for implants should focus on these factors to improve functional outcome after surgery.

MaxLink: network-based prioritization of genes tightly linked to a disease seed set.

UNLABELLED: MaxLink, a guilt-by-association network search algorithm, has been made available as a web resource and a stand-alone version. Based on a user-supplied list of query genes, MaxLink identifies and ranks genes that are tightly linked to the query list. This functionality can be used to predict potential disease genes from an initial set of genes with known association to a disease. The original algorithm, used to identify and rank novel genes potentially involved in cancer, has been updated to use a more statistically sound method for selection of candidate genes and made applicable to other areas than cancer. The algorithm has also been made faster by re-implementation in C++, and the Web site uses FunCoup 3.0 as the underlying network. AVAILABILITY AND IMPLEMENTATION: MaxLink is freely available at http://maxlink.sbc.su.se both as a web service and a stand-alone application for download.

Fast and accurate database searches with MS-GF+Percolator.

One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.

Fastphylo: fast tools for phylogenetics.

BACKGROUND: Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances. RESULTS: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency. CONCLUSIONS: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies.

InParanoid 6: eukaryotic ortholog clusters with inparalogs.

The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted in 2 642 187 pairwise ortholog groups in total. The orthology-based species relations are presented in an orthophylogram. InParanoid clusters contain one or more orthologs from each of the two species. Multiple orthologs in the same species, i.e. inparalogs, result from gene duplications after the species divergence. A new InParanoid website has been developed which is optimized for speed both for users and for updating the system. The XML output format has been improved for efficient processing of the InParanoid ortholog clusters.